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4. Tissue Resources for the Functional Annotation of Animal Genomes

Author

Tixier-Boichard, Michèle, Fabre, Stéphane, Dhorne-Pollet, Sophie, Goubil, Adeline, Acloque, Hervé, Vincent-Naulleau, Silvia, Ross, Pablo, Wang, Ying, Chanthavixay, Ganrea, Cheng, Hans, Ernst, Catherine, Leesburg, Vicki, Giuffra, Elisabetta, Zhou, Huaijun, Group, Collaborative Working, Taragnat, Catherine, Berri, Cecile, Jardet, Déborah, Godet, Estelle, Laurent, Fabrice, Gomot, Gilles, Dardente, Hughes, Grasseau, Isabelle, Dubois, Jean-Philippe, Gautron, Joel, Gérard, Nadine, Quéré, Pascale, Lavocat, Roger-Paul, Dalbies-Tran, Rozenn, Métayer, Sonia, Marthey, Sylvain, Coustham, Vincent, and Druart, Xavier

Subjects
Biological Sciences, Genetics, tissue sampling, repository, mammals, bird, cryopreservation, genome, Collaborative Working Group, Clinical Sciences, Law
Abstract

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Published
2021

7. GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

Author

Tuggle, Christopher K, Giuffra, Elisabetta, White, Stephen N, Clarke, Laura, Zhou, Huaijun, Ross, Pablo J, Acloque, Hervé, Reecy, James M, Archibald, Alan, Bellone, Rebecca R, Boichard, Michèle, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard PMA, Delany, Mary E, Finno, Carrie J, Groenen, Martien AM, Hayes, Ben, Lunney, Joan K, Petersen, Jessica L, Plastow, Graham S, Schmidt, Carl J, Song, Jiuzhou, and Watson, Mick

Subjects
Biological Sciences, Genetics, Animals, Animals, Domestic, Congresses as Topic, District of Columbia, Genome, Genomics, International Cooperation, Reference Standards, data coordination centre, data sharing, metanalysis, Zoology, Veterinary Sciences, Dairy & Animal Science, Veterinary sciences
Abstract

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Published
2016

14. Modeling Global Genomic Instability in Chronic Myeloid Leukemia (CML) Using Patient-Derived Induced Pluripotent Stem Cells (iPSCs)

Author

Telliam, Gladys, primary, Desterke, Christophe, additional, Imeri, Jusuf, additional, M’kacher, Radhia, additional, Oudrhiri, Noufissa, additional, Balducci, Estelle, additional, Fontaine-Arnoux, Micheline, additional, Acloque, Hervé, additional, Bennaceur-Griscelli, Annelise, additional, and Turhan, Ali G., additional

Published
2023
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15. A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits

Author

Osteil, Pierre, Moulin, Anaïs, Santamaria, Claire, Joly, Thierry, Jouneau, Luc, Aubry, Maxime, Tapponnier, Yann, Archilla, Catherine, Schmaltz-Panneau, Barbara, Lecardonnel, Jérôme, Barasc, Harmonie, Mouney-Bonnet, Nathalie, Genthon, Clémence, Roulet, Alain, Donnadieu, Cécile, Acloque, Hervé, Gocza, Elen, Duranthon, Véronique, Afanassieff, Marielle, and Savatier, Pierre

Published
2016
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16. Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues

Author

Crespo-Piazuelo, Daniel, Acloque, Hervé, González-Rodríguez, Olga, Mongellaz, Mayrone, Mercat, Marie-José, Bink, Marco, Huisman, Abe, Ramayo-Caldas, Yuliaxis, Sánchez, Juan Pablo, Ballester, Maria, Producció Animal, Genètica i Millora Animal, Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain (IRTA), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du Porc (IFIP), Hendrix Genetics Research Technology & Services B.V., Boxmeer (5830 AC), The Netherlands, Hendrix Genetics (HG), Hypor B.V., Boxmeer (5830 AC), The Netherlands (HYPOR), oxford university press, European Project: 817998,H2020,H2020-EU.3.2.1.1., and H2020-EU.3.2.3.1.,GENE-SWitCH(2019)

Subjects
pig, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, hotspot, RNA-Seq, eQTL, eQTL hotspot pig RNA-Seq WGS, WGS
Abstract

Background In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle. Results More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3′UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5′-GATCCNGYGTTGCYG-3′ and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region. Conclusions The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes. info:eu-repo/semantics/publishedVersion

Published
2023
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17. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Published
2019
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18. 550. Extensive functional genomics information from early developmental time points for pig and chicken

Author

Acloque, Hervé, Harrison, P.W., Lakhal, W., Martin, F., Archibald, A.L., Beinat, M., Davey, M., Djebali, S., Foissac, S., Guizard, S., Guyomar, C., Kuo, R., Kurylo, C., Madsen, O., Miedzinska, K., Mongellaz, M., Smith, J., Sokolov, A., de Vos, J., Giuffra, E., Watson, M., Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Epigenetics R&D, The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Institut de Recherche en Santé Digestive (IRSD ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), European Project: 817998,H2020,H2020-EU.3.2.1.1., and H2020-EU.3.2.3.1.,GENE-SWitCH(2019)

Subjects
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio]
Abstract

International audience; The global Functional Annotation of Farm Animal Genomes initiative (FAANG) aims to improve animal breeding by improved genomic prediction via integration of functional genomics information. The GENE-SWitCH project has produced extensive functional genomics information for a variety of important tissues at early embryonic timepoints for both chickens and pigs. These datasets will be integrated to produce both tissue and time-point specific transcript, gene, and regulatory annotation for both species. In this paper, we describe the aims of the project, and the initial release of both raw and processed data.

Published
2022
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24. In utero exposure to metformin reduces the fertility of male offspring in adulthood

Author

Faure, Mélanie C., Khoueiry, Rita, Quanico, Jusal, Acloque, Hervé, Guerquin, Marie-Justine, Bertoldo, Michael J., Chevaleyre, Claire, Ramé, Christelle, Fournier, Isabelle, Salzet, Michel, Dupont, Joëlle, Froment, Pascal, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U 1192 (PRISM), Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), U967, Laboratoire de Développement des Gonades, Institut National de la Santé et de la Recherche Médicale (INSERM), University of New South Wales [Sydney] (UNSW), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INSERM, Université de Lille, Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U1192, and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Adult, Male, endocrine system diseases, Endocrinology, Diabetes and Metabolism, [SDV]Life Sciences [q-bio], digestive, oral, and skin physiology, nutritional and metabolic diseases, embryo, testis, Endocrinology, Fertility, pregnancy, metformin, spermatozoa, ovary, Humans, Hypoglycemic Agents, reproductive and urinary physiology, Original Research
Abstract

International audience; Metformin is a drug used for the treatment of type 2 diabetes and disorders associated with insulin resistance. Metformin is also used in the treatment of pregnancy disorders such as gestational diabetes. However, the consequences of foetal exposure to metformin on the fertility of exposed offspring remain poorly documented. In this study, we investigated the effect of in utero metformin exposure on the fertility of female and male offspring. We observed that metformin is detectable in the blood of the mother and in amniotic fluid and blood of the umbilical cord. Metformin was not measurable in any tissues of the embryo, including the gonads. The effect of metformin exposure on offspring was sex specific. The adult females that had been exposed to metformin in utero presented no clear reduction in fertility. However, the adult males that had been exposed to metformin during foetal life exhibited a 30% reduction in litter size compared with controls. The lower fertility was not due to a change in sperm production or the motility of sperm. Rather, the phenotype was due to lower sperm head quality – significantly increased spermatozoa head abnormality with greater DNA damage – and hypermethylation of the genomic DNA in the spermatozoa associated with lower expression of the ten-eleven translocation methylcytosine dioxygenase 1 (TET1) protein. In conclusion, while foetal metformin exposure did not dramatically alter gonad development, these results suggest that metabolic modification by metformin during the foetal period could change the expression of epigenetic regulators such as Tet1 and perturb the genomic DNA in germ cells, changes that might contribute to a reduced fertility.

Published
2021
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25. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Author

Giuffra, Elisabetta, Tuggle, Christopher K., Archibald, A.L., ACLOQUE, Hervé, Chamberlain, Amanda J., Cochrane, Guy, Daetwyler, Hans D., Djebali Quelen, Sarah, Eory, Lel, Foissac, Sylvain, Goddard, Michael E., Groenen, Martien A.M., Halstead, Michelle, Harrison, Peter W., Hayes, B.J., Kern, Colin, Khatib, Hassan, Kuo, Richard I., MacHugh, David E., MacLeod, I.M., Madsen, Ole, Reecy, Mark James, Ross, Pablo, J., Watson, Mick, Wells, Jerry M., Zhou, H.J., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Iowa State University (ISU), University of Edinburgh, Dept Econ Dev Jobs Transport & Resources, European Molecular Biology Laboratory European Bioinformatics Institute, La Trobe University, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Melbourne, Wageningen University and Research Centre (WUR), University of California [Davis] (UC Davis), University of California, University of Queensland [Brisbane], University of Wisconsin-Madison, University College Dublin (UCD), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Epigenomics, 0301 basic medicine, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], domesticated animal, Genotype, Genomics, Computational biology, Animal Breeding and Genomics, Biology, Genome, genomic selection, 03 medical and health sciences, Annotation, Genome editing, functional genomic, Genetics, Animals, genome editing, Fokkerij en Genomica, Epigenetics, Gene Editing, 2. Zero hunger, epigenetics, General Veterinary, 0402 animal and dairy science, Molecular Sequence Annotation, 04 agricultural and veterinary sciences, genotype-to-phenotype, 040201 dairy & animal science, Chromatin, Phenotype, 030104 developmental biology, domesticated animals, Animals, Domestic, DNA methylation, WIAS, Animal Science and Zoology, functional genomics, Functional genomics, epigenetic, Biotechnology
Abstract

International audience; Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

Published
2019
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29. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species

Author

Jehl, Frédéric, primary, Degalez, Fabien, additional, Bernard, Maria, additional, Lecerf, Frédéric, additional, Lagoutte, Laetitia, additional, Désert, Colette, additional, Coulée, Manon, additional, Bouchez, Olivier, additional, Leroux, Sophie, additional, Abasht, Behnam, additional, Tixier-Boichard, Michèle, additional, Bed’hom, Bertrand, additional, Burlot, Thierry, additional, Gourichon, David, additional, Bardou, Philippe, additional, Acloque, Hervé, additional, Foissac, Sylvain, additional, Djebali, Sarah, additional, Giuffra, Elisabetta, additional, Zerjal, Tatiana, additional, Pitel, Frédérique, additional, Klopp, Christophe, additional, and Lagarrigue, Sandrine, additional

Published
2021
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30. BMAL1 Knockdown Leans Epithelial–Mesenchymal Balance toward Epithelial Properties and Decreases the Chemoresistance of Colon Carcinoma Cells

Author

Zhang, Yuan, primary, Devocelle, Aurore, additional, Desterke, Christophe, additional, de Souza, Lucas Eduardo Botelho, additional, Hadadi, Éva, additional, Acloque, Hervé, additional, Foudi, Adlen, additional, Xiang, Yao, additional, Ballesta, Annabelle, additional, Chang, Yunhua, additional, and Giron-Michel, Julien, additional

Published
2021
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37. Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

Author

Feron, Romain, primary, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Roques, Céline, additional, Bouchez, Olivier, additional, Eché, Camille, additional, Valière, Sophie, additional, Donnadieu, Cécile, additional, Haffray, Pierrick, additional, Bestin, Anastasia, additional, Morvezen, Romain, additional, Acloque, Hervé, additional, Euclide, Peter T., additional, Wen, Ming, additional, Jouano, Elodie, additional, Schartl, Manfred, additional, Postlethwait, John H., additional, Schraidt, Claire, additional, Christie, Mark R., additional, Larson, Wesley A., additional, Herpin, Amaury, additional, and Guiguen, Yann, additional

Published
2020
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40. MOESM1 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Abstract

Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).

Published
2019
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42. The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

Author

Mey Anne, Acloque Hervé, Lerat Emmanuelle, Gounel Sébastien, Tribollet Violaine, Blanc Sophie, Curton Damien, Birot Anne-Marie, Nieto M Angela, and Samarut Jacques

Subjects
Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background Long terminal repeats (LTR) from endogenous retroviruses (ERV) are source of binding sites for transcription factors which affect the host regulatory networks in different cell types, including pluripotent cells. The embryonic epiblast is made of pluripotent cells that are subjected to opposite transcriptional regulatory networks to give rise to distinct embryonic and extraembryonic lineages. To assess the transcriptional contribution of ERV to early developmental processes, we have characterized in vitro and in vivo the regulation of ENS-1, a host adopted and developmentally regulated ERV that is expressed in chick embryonic stem cells. Results We show that Ens-1 LTR activity is controlled by two transcriptional pathways that drive pluripotent cells to alternative developmental fates. Indeed, both Nanog that maintains pluripotency and Gata4 that induces differentiation toward extraembryonic endoderm independently activate the LTR. Ets coactivators are required to support Gata factors' activity thus preventing inappropriate activation before epigenetic silencing occurs during differentiation. Consistent with their expression patterns during chick embryonic development, Gata4, Nanog and Ets1 are recruited on the LTR in embryonic stem cells; in the epiblast the complementary expression of Nanog and Gata/Ets correlates with the Ens-1 gene expression pattern; and Ens-1 transcripts are also detected in the hypoblast, an extraembryonic tissue expressing Gata4 and Ets2, but not Nanog. Accordingly, over expression of Gata4 in embryos induces an ectopic expression of Ens-1. Conclusion Our results show that Ens-1 LTR have co-opted conditions required for the emergence of extraembryonic tissues from pluripotent epiblasts cells. By providing pluripotent cells with intact binding sites for Gata, Nanog, or both, Ens-1 LTR may promote distinct transcriptional networks in embryonic stem cells subpopulations and prime the separation between embryonic and extraembryonic fates.

Published
2012
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43. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kévin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, CRISCI, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, González, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaëlle, Mompart, Florence, Quéré, Pascale, Robelin, David, San Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard - Van Der Laan, Marie-Helene, Klopp, Christophe, Tixier-Boichard, Michele, ACLOQUE, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), iRCM, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Livestock, Hi-C, [SDV]Life Sciences [q-bio], Functional annotation, [INFO]Computer Science [cs], ATAC-seq, RNA-seq, [MATH]Mathematics [math]
Abstract

Article publié dans BMC Biology. Disponible ici : https://prodinra.inra.fr/record/491694; Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays allowed to considerably extend the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species adds up to previous findings in model animals. Overall, these results emphasize the value of FAANG for the research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2018
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44. Chronic circadian disruption modulates breast cancer cell stemness and their immune microenvironment to drive metastasis in mice

Author

Hadadi, Eva, primary, Taylor, William, additional, Li, Xiaomei, additional, Aslan, Yetki, additional, Villote, Marthe, additional, Rivière, Julie, additional, Duvallet, Gaelle, additional, Auriau, Charlotte, additional, Dulong, Sandrine, additional, Letron, Isabelle Raymond, additional, Provot, Sylvain, additional, Bennaceur-Griscelli, Annelise, additional, and Acloque, Hervé, additional

Published
2019
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45. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Author

Feron, Romain, primary, Zahm, Margot, additional, Cabau, Cédric, additional, Klopp, Christophe, additional, Roques, Céline, additional, Bouchez, Olivier, additional, Eché, Camille, additional, Valière, Sophie, additional, Donnadieu, Cécile, additional, Haffray, Pierrick, additional, Bestin, Anastasia, additional, Morvezen, Romain, additional, Acloque, Hervé, additional, Euclide, Peter T., additional, Wen, Ming, additional, Jouano, Elodie, additional, Schartl, Manfred, additional, Postlethwait, John H., additional, Schraidt, Claire, additional, Christie, Mark R., additional, Larson, Wes, additional, Herpin, Amaury, additional, and Guiguen, Yann, additional

Published
2019
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47. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Author

Foissac, Sylvain, Djebali Quelen, Sarah, ACLOQUE, Hervé, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Derrien, Thomas, Drouet, Françoise, Esquerre, Diane, Fabre, Stéphane, Gaspin, Christine, GONZALEZ, Ignacio, Goubil, Adeline, Klopp, Christophe, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Mompart, Florence, Munyard, Kylie, Muret, Kévin, Pollet, Sophie, Quéré, Pascale, Rau, Andrea, Robelin, David, San Cristobal, Magali, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Villa-Vialaneix, Nathalie, Vincent-Naulleau, Silvia, Zytnicki, Matthias, Pinard - Van Der Laan, Marie-Helene, Lagarrigue, Sandrine, Giuffra, Elisabetta, Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FR-AgENCODE, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
multispecies, Hi-C, [SDV]Life Sciences [q-bio], Multispecies, Biologie animale, Functional annotation of animal genome (FAANG), functional annotation of animal genome (FAANG), ATAC-seq, RNA-seq
Abstract

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals.

Published
2017

48. Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species

Author

Muret, Kévin, Djebali Quelen, Sarah, Derrien, Thomas, Cabau, Cédric, Klopp, Christophe, Esquerre, Diane, Munyard, Kylie, Tosser-Klopp, Gwenola, Acloque, Hervé, Giuffra, Elisabetta, Foissac, Sylvain, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UNIV-RENNES), Sigenae, Institut National de la Recherche Agronomique (INRA), Plateforme Genotoul, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Fr-Agencode, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UR), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Animal biology, Multispecies, Comparative genomics, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, Functional Annotation of Animal Genomes (FAANG), RNA-seq, Long non-coding RNAs
Abstract

Understanding genome-to-phenome relationships requires deep and cross-disciplinary genetic analyses among which functional annotation provides crucial insights. The development of High Throughput Sequencing and RNA-seq now help us to find a large number of heterogeneous and low-expressed transcripts known to be long non-coding RNAs (lncRNAs). One of the aims of the FAANG pilot project ‘FR-AgENCODE’ is to identify and characterise the long non-coding RNAs of multiple tissues and cell lines in 4 farm animals (chicken, bovine, pig and goat) of both sexes. Here, we focus our analysis on the liver tissue and two blood T-cell types (CD3+CD4+, CD3+CD8+) where samples were collected through 4 biological replicates (2 males and 2 females). It allows us to compare lncRNA repertoires between tissues, sex and species in relation with fundamental biological functions like energy storage and immunity. High depth strand-specific RNA-seq produced ~200M paired-end reads for each of the 16 RNA-seq datasets. After transcriptome reconstruction, we used the recently published FEELnc program (Wucher et al., 2017, Nucleic Acid Research) to identify lncRNAs longer than 200 bp and without protein-coding capabilities. FEELnc also classifies lncRNAs based on their genomic localizations with respect to the ENSEMBL protein-coding annotation: intergenic lncRNAs are categorized depending on the distance and orientation with respect to the closest mRNAs and the intragenic lncRNAs are extracted based on their overlap with mRNAs exons and introns. We will report these lncRNA repertoires in terms of intergenic/ intragenic lncRNA class, structure and expression and comparing these features between livestock species, tissues and sexes. By profiling the transcriptional landscape of lncRNAs in these 4 species, this data will further contribute to the global action for annotating functional elements of livestock genomes.

Published
2017

49. Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions

Author

Djebali Quelen, Sarah, Munyard, Kylie, Villa-Vialaneix, Nathalie, Cabau, Cédric, Rau, Andrea, CRISCI, Elisa, Derrien, Thomas, Klopp, Christophe, Zytnicki, Matthias, Lagarrigue, Sandrine, ACLOQUE, Hervé, Foissac, Sylvain, Giuffra, Elisabetta, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Fr-Agencode, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)

Subjects
Pigs and related species, Hi-C, [SDV]Life Sciences [q-bio], Functional Annotation of Animal Genomes (FAANG), ATAC-seq, RNA-seq
Abstract

In the context of the FAANG pilot project ‘FR-AgENCODE’ to improve the functional annotation of livestock genomes, we characterised the transcriptome and the chromatin accessibility of pig hepatocytes and two types of lymphocytes. More specifically, CD3+CD4+ (‘CD4’) and CD3+CD8+ (‘CD8’) T-cells were sorted from the blood of two male and two female Large White adult pigs. These samples, along with liver samples from the same animals, were processed by strand-oriented RNA-seq and ATAC-seq experiments. Principal Component Analyses on log-transformed TMM-normalized read counts in genes (from RNA-seq) and regions of chromatin accessibility (from ATAC-seq) consistently highlighted the variability between liver and the T-cells, and to a lesser extent within T-cells (CD4 v. CD8), as well as between the male and female samples. Comparative analyses identified differentially expressed genes between cell types as well as potential regulatory sites from differentially accessible chromatin regions. As expected, ontology annotations of differentially expressed genes were enriched for either immunity- or metabolism-related terms. Interestingly, correlations between gene expression and promoter accessibility across samples were enriched for both extreme positive and negative values, which suggests that ATAC-seq can efficiently capture distinct regulatory mechanisms of gene expression. Candidate enhancers and repressors were identified by comparing ATAC-seq regions with predicted binding sites of 500+ transcription factors. By integrating these results with those from Hi-C chromosome con-formation capture on the liver samples, we further characterised the differences between ‘active’ and ‘repressed’ topological domains in terms of functional features, including gene density and general chromatin accessibility. Altogether, these results lead to a better un-derstanding of the molecular mechanisms involved in pig immune and metabolic functions, and illustrate a useful contribution to the functional annotation effort of the FAANG initiative.

Published
2017

50. Une nouvelle facette du génome de poule : les genes 'longs non-codants'

Author

Muret, Kévin, Klopp, Christophe, Wucher, Valentin, Esquerre, Diane, Legeai, Fabrice, Lecerf, Frédéric, Désert, Colette, Boutin, Morgane, Jehl, Frédéric, Acloque, Hervé, Giuffra, Elisabetta, Djebali Quelen, Sarah, Foissac, Sylvain, Derrien, Thomas, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Sigenae, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UNIV-RENNES), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier (UT3), Genotoul, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UR), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
base de données, NCBI, broilers, classification, [SDV.BA]Life Sciences [q-bio]/Animal biology, tissu adipeux, liver function tests, Ensembl, RNA-seq, foie, transcriptome, poulet de chair, adipose tissue
Abstract

Recent works in humans and model organisms have shown a massive new type of genes: genes transcribed intolong RNAs (≥ 200 nt) but not coding for proteins - these genes are called long noncoding RNA genes (lncRNA).These lncRNAs are a major component of the transcriptome and only a small fraction of them is described inpublic databases. Our study conducted on chicken shows that transcriptomic sequencing (RNA-Seq) on multiplebiological replicates of two tissues (liver and adipose tissue) allows us to predict a lncRNA catalog for these twotissues more exhaustive than lncRNAs catalog available in public databases. We also confirm that chickenlncRNA features are similar to those of human and murine lncRNAs described in the literature (shortertranscripts, less exons, sequences less conserved across species, more tissue-specific expression and lowerexpression than protein coding RNAs (mRNA)). In conclusion, we provide a comprehensive lncRNA repertoirein the chicken liver and adipose tissue and we highlighte a new lncRNA-mRNA pair in divergent position in thechicken genome (as in the human genome), highly co-expressed suggesting a common regulation mechanismthrough a bidirectional promoter and probably involved in cholesterol metabolism.; De récents travaux effectués chez l’homme et des organismes modèles ont montré l’existence massive d’unnouveau type de gènes : des gènes transcrits en longs ARN (≥ 200 nt) mais ne codant pas de protéine – ces gènes sont appelés gènes à ARN longs non-codants (ARNlnc). Ces ARNlnc sont une composante majeure dutranscriptome et seule une petite fraction de ces ARNlnc est décrite aujourd’hui dans les bases de donnéespubliques. Nos travaux sur les ARNlnc de poule ont permis de montrer que le séquençage de transcrits (RNASeq) sur plusieurs réplicats biologiques de deux tissus (foie et tissu adipeux) permet de prédire un catalogue d’ARNlnc plus exhaustif pour les tissus considérés que ce qui est proposé dans les bases de données. Nous avons pu confirmer également que les caractéristiques des ARNlnc de poule sont similaires à celles décrites chez la souris ou chez l’Homme (transcrits plus courts, moins d’exons, séquences moins conservées entre les espèces, expression plus tissu spécifique et moins importante que les ARN codant pour des protéines (ARNm)). Nous mettons également en lumière un couple d’ARNlnc et ARNm (DHCR24) adjacent sur le génome et en position divergente dont l’expression est fortement corrélée et dont la position est conservée chez l’Homme suggérant un mécanisme de régulation commun via un promoteur dit « bi-directionnel » qui serait impliqué dans la synthèse du cholestérol.

Published
2017

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